I have question related to obtaining files from different folders using shell command
I have the following directory name
TC1-T1
TC1-T2
TC1-T3
TC1-T4
I want to obtain the files from 1st directory (TC1-T1) , 2nd directory (TC1-T2), and then the loop goes to TC1-T3 (3rd) and 4th directory as (TC1-T4). I wrote the following code but it did not work. I am looking forward if someone can help me in editing the shell command.
for pair in "TC"{1..2}-"T"{1..10}; do for i in $pair; do printf ${i}+1 printf "\n" done done
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How to loop over files in directory and change path and add suffix to filename
(6 answers)
Closed 4 years ago.
New to Linux here, sorry for the (easy?) question:
I have a script in Linux called script_run that works fine if I run it once and manually designate filenames. The script reads an input file, interpolates the data, and then saves the interpolated data to an output file. I'd like the output file to have the same name, except with a "_interp" added. I want to automate the script to run for all files in the file folder directory. How do I do this? My attempt is below, and I am running the script in the file folder directory, but it fails to loop. Thank you for your help!
FILEFOLDER=$*
for FILES in $FILEFOLDER
do
script_run "
[--input ${FILES}]
[WriterStd --output tmp_output_${FILES}.txt]"
cat tmp_output_${FILES}.txt >> output_${FILES}_interp.txt
done
#!/bin/bash
FILES=`ls *.*`
for FILE in $FILES
do
script_run "[--input ${FILE}] [WriterStd --output tmp_output_${FILE}.txt]"
cat tmp_output_${FILE}.txt >> output_${FILE}_interp.txt
done
btw what's with this strange annotation [--input ${FILE}] ? Does your script explicitly requires a format like that?
I have a RedHat linux box and I had written a script in the past to move files from one location to another with a specific text in the body of the file.
I typically only write scripts once a year so every year I forget more and more... That being said,
Last year I wrote this script and used it and it worked.
For some reason, I can not get it to work today and I know it's a simple issue and I shouldn't even be asking for help but for some reason I'm just not looking at it correctly today.
Here is the script.
ls -1 /var/text.old | while read file
do
grep -q "to.move" $file && mv $file /var/text.old/TBD
done
I'm listing all the files inside the /var/text.old directory.
I'm reading each file
then I'm grep'ing for "to.move" and holing the results
then I'm moving the resulting found files to the folder /var/text.old/TBD
I am an admin and I have rights to the above files and folders.
I can see the data in each file
I can mv them manually
I have use pwd to grab the correct spelling of the directory.
If anyone can just help me to see what the heck I'm missing here that would really make my day.
Thanks in advance.
UPDATE:
The files I need to move do not have Whitespaces.
The Error I'm getting is as follows:
grep: 9829563.msg: No such file or directory
NOTE: the file "982953.msg" is one of the files I need to move.
Also note: I'm getting this error for every file in the directory that I'm listing.
You didn't post any error, but I'm gonna take a guess and say that you have a filename with a space or special shell character.
Let's say you have 3 files, and ls -1 gives us:
hello
world
hey there
Now, while splits on the value of the special $IFS variable, which is set to <space><tab><newline> by default.
So instead of looping of 3 values like you expect (hello, world, and hey there), you loop over 4 values (hello, world, hey, and there).
To fix this, we can do 2 things:
Set IFS to only a newline:
IFS="
"
ls -1 /var/text.old | while read file
...
In general, I like setting IFS to a newline at the start of the script, since I consider this to be slightly "safer", but opinions on this probably vary.
But much better is to not parse the output of ls, and use for:
for file in /var/text.old/*`; do
This won't fork any external processes (piping to ls to while starts 2), and behaves "less surprising" in other ways. See here for some examples.
The second problem is that you're not quoting $file. You should always quote pathnames with double quoted: "$file" for the same reasons. If $file has a space (or a special shell character, such as *, the meaning of your command changes:
file=hey\ *
mv $file /var/text.old/TBD
Becomes:
mv hey * /var/text.old/TBD
Which is obviously very different from what you intended! What you intended was:
mv "hey *" /var/text.old/TBD
Currently I am trying to run MRI software (TBSS) on imaging files(scan.nii.gz) on the Linux command line.
The scans are all stored in separate folders for different participants and the file names are identical,so:
/home/scans/participant1/scan.nii.gz
/home/scans/participant2/scan.nii.gz
/home/scans/participant3/scan.nii.gz
What this software does is it creates the result of the analysis in the current working directory.Since the scans have the same image name, they get overwritten al the time.
I would like to loop through all the participant folders, make it my working directory and then execute the tbss command, which is simply tbss_1_preproc scan.nii.gz. In this way, the file will be stored in the current working directory,which is the participant directory.
Is there any sensible way of doing this in Linux ?
Thanks so much !
Try it in BASH. The code below is untested, but it should give you a clue
#! /bin/bash
find . -name scan.nii.gz | while read line
do
cd $(dirname "${line}")
tbss_1_preproc $(basename "${line}")
done
Put it in a file and make it executable. Copy it to your scans folder and execute it.
I want to copy a file from a directory using shell script
Suppose I save the directory and file name seperately as
dir=/home/user/directory/
file=file_1
to copy the file Im using this command in my script
cp $dir$file .
But I get this error
/bin/cp omitting directory '/home/user/directory'
I have tried all combination eg. omitted the trail backslah from variable dir, etc but nothings working. I cant understand what is wrong with this code. Pleas help
Maybe the command $dir$file is not getting unpacked in the shell (ie only the directory variable is getting unpacked, not the file variable)!!!!!
It looks like you are having problem with expansion in cp $dir$file . In order to prevent possible problems, it is better to protect your variable with braces and double quote the full path/file to make sure you don't get caught by spaces in either the filename or heaven forbid the user's dirname:
cp "${dir}${file}" .
This will prevent the possibility the second $ is missed. Also make sure you have read access to other users /home (if you are root or using sudo you should be fine)
If you see this, when you somehow assign an empty string to file somewhere. Search your script for file= and unset file.
You can also debug this by adding
echo ".${file}."
in the line before the cp command. I'm pretty sure it prints .., i.e. the variable is empty or doesn't exist.
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How do I modify my user PROFILE file to append a scripts folder I created to the end of my PATH variable?
I am not totally sure what this means. Can anyone explain?
In unix/linux systems, you have a user id ('john') and a home directory ('/home/john'). The home directory has an abbreviation, the tilde: ~ (at the start of a directory path) means the same as your home directory ("/home/john").
In the home directory are several files that begin with a period (aka dot files because they start with a dot, i.e., a period). When you log in, the shell (i.e., the program that processes the command line when you type commands) that is started to supply you a command line looks for these files and reads them, using their content to initialize your shell environment. You can see these files (if they exist) by entering these commands at the command line:
cd
ls -a
The cd with no args means 'change the current directory to be my HOME directory. The ls command lists files in a directory (among other things); the -a option says 'show hidden files'. Hidden files are those that start with a period - this is the convention used in unix/linux to 'hide' files.
The .profile (said out loud it's often pronounced 'dot profile') file is one such dot file used for initializing your environment.
The PATH environment variable is used by the shell to search for executable files (programs).
You can google for 'how to update PATH in profile' and similar to learn more about the topic.
Here is a typical snippet found in a .profile file; its purpose is to allow you to run programs that are stored in the directory /usr/mypackage/bin.
PATH="/usr/mypackage/bin:$PATH"
export PATH
Putting a directory on the PATH allows you to type just a program name ('myprogram') in place of the longer form ('/usr/mypackage/bin/myprogram').
You can see the effect of this snippet using echo $PATH; it will show the entire value of the PATH variable. The value should be a list of paths (directories) separated by colon. A simple example:
echo $PATH
/usr/mypackage/bin:/usr/bin:/bin
That should give you a foothold to begin investigating the details. Trying searching for topics like 'how do I set up my linux/unix login', 'what is .profile file', etc., to learn more.
It's advisable to use double-quotes when setting the value of PATH to encapsulate any 'usual' characters that may be in the names of the items in the path. Single quotes are not suitable for this as they will prevent the evaluation of $PATH (which is what supplies your existing path when defining your new path value). For more on quotes, here is one discussion of single vs double quotes
Built-in programs like cat and cd simply work by entering the command. However, they are located in a certain folder, such as /usr/bin/. Try for yourself, and see which folder cat is located in, by entering which cat.
When you type in such command, your shell needs a list of folders in which it has to look for the command just entered. It used the $PATH variable for this, which stores this list. You can see it by entering echo $PATH.
Now, if you close your shell, the $PATH variable is gone. When you reopen your shell, it starts a certain amount of scripts, one of them being the .profile script. In this script, the $PATH variable is loaded. Therefore, you could adjust the .profile file in order to save your $PATH permanently. To do so, simply edit this file and edit the line where $PATH is defined (e.g. pico ~/.profile).
In your particular case, adding your scripts folder to the $PATH like this, will make you can simply write the name of your script instead of the whole pad when you want to launch one.
The PATH variable stores the list of directories the shell searches for programs/commands when you try to run them. You can access its value from the command line by typing:
echo $PATH
Be careful when modifying it, otherwise you could interfere with your ability to run programs from the command line. To add a new directory without modifying the original value, you could put a line in your file such as:
PATH=$PATH:/directory_to_add
where 'directory_to_add' is the directory you want to add to the path ($PATH tells the shell to insert the value of PATH). Then, if you type the name of one of the scripts in the folder at the command line, it will run without having to type the full pathname (as long as it has execute permission).
Note - your profile file can be found at ~/.profile, and you can add the line above with a text editor and resave the file. Then, from your home directory, type sh ./.profile, and your path should now include the desired directory.